Central midfielder Mowatt, who played every minute of Barnsley’s League One promotion campaign, had to come off during the 2-0 loss to Sheffield Wednesday at Hillsborough on Saturday.
If he cannot face Charlton Athletic tomorrow, his place is likely to be taken by 19-year-old Callum Styles, or captain Mike Bahre could drop back from attacking midfield to partner Cameron McGeehan.
Coach Dale Tonge said: “We have players who can go into that position, like Mikey and Callum. We’re not negative about it at all, we see it as an opportunity for someone to come in and stake a claim. We haven’t been made aware that the club is looking to sign a new player in that position.
“We’re not sure of the nature of his injury. It’s a rare one. He felt it before the Sheffield Wednesday game in training. He’s a doubt for the weekend. He will be assessed and we’ll see how he is. We have had a couple of scans on him and we’re waiting for the results to see if it will be short or long-term.”
Mowatt’s injury adds to the problems in central midfield with Kenny Dougall still out, but winger Jordan Green is back in training. Jacob Brown is making ‘good progress’ and could return to full training before the end of the month.
Meanwhile, deadline day signings Patrick Schmidt and Clark Oduor are being drilled in Barnsley’s style of play. Tonge said: “We’re trying to get them up to speed. Patrick is a little bit behind so he’s doing extra work. We are doing a lot of individual work with both of them in terms of how we play. Hopefully in the next week or so they will be integrated. This weekend might be too soon but we will see.”